Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › ab inito memberane(error in alignblast.pl)
- This topic has 6 replies, 4 voices, and was last updated 12 years, 3 months ago by
Anonymous.
-
AuthorPosts
-
-
May 4, 2011 at 6:41 am #897
Anonymous
Hello everyone:
When I run “/rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /rosetta/blast/bin/blastpgp /rosetta/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl”,I got the error that:
[root@localhost input]# /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /rosetta/blast/bin/blastpgp /rosetta/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl
Error in alignblast.pl: blast output file t2.blast truncated:
readline() on closed filehandle MSA at /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl line 91.
2 0 0 -
May 6, 2011 at 8:52 am #5543
Anonymous
Who can help me,I am very anxiety,I can’t solve the error.Even if I re-download the db include nr00,nr01,nr02,nr03,nr04,nr05,I decompress them and put them into nr directory,I run “/rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /blast/bin/blastpgp /blast/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl”,it just like running,but I also got the error:
[root@localhost input]# /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /blast/bin/blastpgp /blast/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl
Running:
/blast/bin/blastpgp -i t2.fasta -d /blast/nr -j 2 -h 0.001 -b5000 -v5000 -o t2.blast
Error in alignblast.pl: blast output file t2.blast truncated:
readline() on closed filehandle MSA at /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl line 91.
2 0 0 -
May 6, 2011 at 6:30 pm #5544
Anonymous
I have no familiarity with membrane ab initio, so I’m completely guessing here, but it looks like your blast is failing somehow.
See if you can run the printed command (“/blast/bin/blastpgp -i t2.fasta -d /blast/nr -j 2 -h 0.001 -b5000 -v5000 -o t2.blast”) by itself and see what happens. Take a look at the t2.blast output file and see if it looks like it’s supposed to.
Also, I found these posts which may be some help:
http://www.rosettacommons.org/node/1751
http://www.rosettacommons.org/node/2298 -
May 8, 2012 at 12:10 pm #7087
Anonymous
Please see my reply to
http://www.rosettacommons.org/content/membrane-folding-blastpgp-error -
June 8, 2012 at 2:09 pm #7193
Anonymous
I am also getting the same error Error in alignblast.pl: blast output file filename.fasta.out truncated. readline () on closed filehandle MSA at ./run_lips.pl line 92.
Any one got solution for this error?
-
May 10, 2011 at 3:08 am #5554
Anonymous
Hi rmoretti,thank you for your reply,I have read them,but I can’solve the error.Do you have a new solution.
-
May 10, 2011 at 3:25 am #5556
Anonymous
Thank you for the tips, I accidentally solved the problem.
-
-
AuthorPosts
- You must be logged in to reply to this topic.